Mosaic charge coupled device (CCD) or complementary metal oxide semiconductor (CMOS) cameras are crucial for giant telescopes, especially those with a large field of view (FOV). One of the critical determinants of image quality is the flatness of the mosaic focal plane arrays (MFPAs). The MFPAs can only be assembled at room temperature and operated under cryogenic cooling with a vacuum chamber to reduce image noise; however, changes and inhomogeneities in temperature can deform the focal plane and affect the flatness. Under cryogenic conditions, the measurement must be taken through a flat dewar window, which will reduce the measurement precision. To correctly measure the MFPAs under cryogenic conditions, we developed a method called differential triangulation measurement (DTM) using the method of laser triangulation and differential measurement. In this study, the feasibility of the laser triangulation measurement through a flat window using the oblique mode is demonstrated. Furthermore, a differential measurement method using two laser triangulation sensors is adopted to improve the precision of measurement. One sensor is used to scan a precision optical flat as a reference, and the other is used to scan the MFPAs. A flatness calculation method based on the progressive sample consensus algorithm (PROSAC) is used to optimize data processing. A measurement system based on DTM (DTMS) is designed and implemented for the flatness measurement of MFPAs in a vacuum chamber. The measurement precision of the system was verified by measuring an ultrahigh precision gauge step block. The test results show that the measurement error through the flat dewar window is less than 0.5%. Finally, the DTMS is applied in the MFPA flatness measurement of the prime-focus camera of the wide field sky survey telescope (WFST).